301
|
Badcock C. The imprinted brain: how genes set the balance between autism and psychosis. Epigenomics 2012; 3:345-59. [PMID: 22122342 DOI: 10.2217/epi.11.19] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The imprinted brain theory proposes that autism spectrum disorder (ASD) represents a paternal bias in the expression of imprinted genes. This is reflected in a preference for mechanistic cognition and in the corresponding mentalistic deficits symptomatic of ASD. Psychotic spectrum disorder (PSD) would correspondingly result from an imbalance in favor of maternal and/or X-chromosome gene expression. If differences in gene expression were reflected locally in the human brain as mouse models and other evidence suggests they are, ASD would represent not so much an 'extreme male brain' as an extreme paternal one, with PSD correspondingly representing an extreme maternal brain. To the extent that copy number variation resembles imprinting and aneuploidy in nullifying or multiplying the expression of particular genes, it has been found to conform to the diametric model of mental illness peculiar to the imprinted brain theory. The fact that nongenetic factors such as nutrition in pregnancy can mimic and/or interact with imprinted gene expression suggests that the theory might even be able to explain the notable effect of maternal starvation on the risk of PSD - not to mention the 'autism epidemic' of modern affluent societies. Finally, the theory suggests that normality represents balanced cognition, and that genius is an extraordinary extension of cognitive configuration in both mentalistic and mechanistic directions. Were it to be proven correct, the imprinted brain theory would represent one of the biggest single advances in our understanding of the mind and of mental illness that has ever taken place, and would revolutionize psychiatric diagnosis, prevention and treatment - not to mention our understanding of epigenomics.
Collapse
|
302
|
|
303
|
Devlin B, Scherer SW. Genetic architecture in autism spectrum disorder. Curr Opin Genet Dev 2012; 22:229-37. [PMID: 22463983 DOI: 10.1016/j.gde.2012.03.002] [Citation(s) in RCA: 332] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 03/02/2012] [Accepted: 03/05/2012] [Indexed: 01/08/2023]
Abstract
Autism spectrum disorder (ASD) is characterized by impairments in reciprocal social interaction and communication, and by restricted and repetitive behaviors. Family studies indicate a significant genetic basis for ASD susceptibility, and genomic scanning is beginning to elucidate the underlying genetic architecture. Some 5-15% of individuals with ASD have an identifiable genetic etiology corresponding to known chromosomal rearrangements or single gene disorders. Rare (<1% frequency) de novo or inherited copy number variations (CNVs) (especially those that affect genes with synaptic function) are observed in 5-10% of idiopathic ASD cases. These findings, coupled with genome sequencing data suggest the existence of hundreds of ASD risk genes. Common variants, yet unidentified, exert only small effects on risk. Identification of ASD risk genes with high penetrance will broaden the targets amenable to genetic testing; while the biological pathways revealed by the deeper list of ASD genes should narrow the targets for therapeutic intervention.
Collapse
Affiliation(s)
- Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, 3811 O'Hara St., Pittsburgh, PA 15213, USA
| | | |
Collapse
|
304
|
The Simons VIP Consortium. Simons Variation in Individuals Project (Simons VIP): a genetics-first approach to studying autism spectrum and related neurodevelopmental disorders. Neuron 2012; 73:1063-7. [PMID: 22445335 DOI: 10.1016/j.neuron.2012.02.014] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We describe a project aimed at studying a large number of individuals (>200) with specific recurrent genetic variations (deletion or duplication of segment 16p11.2) that increase the risk of developing autism spectrum (ASD) and other developmental disorders. The genetics-first approach augmented by web-based recruitment, multisite collaboration and calibration, and robust data-sharing policies could be adopted by other groups studying neuropsychiatric disorders to accelerate the pace of research.
Collapse
|
305
|
Malhotra D, Sebat J. CNVs: harbingers of a rare variant revolution in psychiatric genetics. Cell 2012; 148:1223-41. [PMID: 22424231 PMCID: PMC3351385 DOI: 10.1016/j.cell.2012.02.039] [Citation(s) in RCA: 593] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Indexed: 12/21/2022]
Abstract
The genetic bases of neuropsychiatric disorders are beginning to yield to scientific inquiry. Genome-wide studies of copy number variation (CNV) have given rise to a new understanding of disease etiology, bringing rare variants to the forefront. A proportion of risk for schizophrenia, bipolar disorder, and autism can be explained by rare mutations. Such alleles arise by de novo mutation in the individual or in recent ancestry. Alleles can have specific effects on behavioral and neuroanatomical traits; however, expressivity is variable, particularly for neuropsychiatric phenotypes. Knowledge from CNV studies reflects the nature of rare alleles in general and will serve as a guide as we move forward into a new era of whole-genome sequencing.
Collapse
Affiliation(s)
- Dheeraj Malhotra
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA 1020103, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 1020103, USA
| | - Jonathan Sebat
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA 1020103, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 1020103, USA
- Department of Cellular Molecular and Molecular Medicine, University of California, San Diego, La Jolla, CA 1020103, USA
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 1020103, USA
| |
Collapse
|
306
|
Kasnauskiene J, Ciuladaite Z, Preiksaitiene E, Matulevičienė A, Alexandrou A, Koumbaris G, Sismani C, Pepalytė I, Patsalis PC, Kučinskas V. A single gene deletion on 4q28.3: PCDH18--a new candidate gene for intellectual disability? Eur J Med Genet 2012; 55:274-7. [PMID: 22450339 DOI: 10.1016/j.ejmg.2012.02.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 02/21/2012] [Indexed: 01/15/2023]
Abstract
We report a boy with severe developmental delay, seizures, microcephaly, hypoplastic corpus callosum, internal hydrocephalus and dysmorphic features (narrow forehead, round face, deep-set eyes, blue sclerae, large and prominent ears, nose with anteverted nares, thin upper lip, small and wide-spaced teeth, hyperextensibility of the elbows, wrists, and fingers, fingertip pads, broad hallux, sacral dimple), carrying a 1.53 Mb interstitial deletion at 4q28.3. The deletion was detected by Agilent 105K oligo-array genome hybridization and involves the genomic region between 137,417,338 and 138,947,282 base pairs on chromosome 4 (NCBI build 36). The alteration was inherited from a healthy mother and contains a single gene, PCDH18 which encodes a cadherin-related neuronal receptor thought to play a role in the establishment and function of cell-cell connections in the brain. Thus, haploinsufficiency of this gene may contribute to altered brain development and associated malformations. We found that this deletion is a private inherited copy number variation that is associated with specific clinical findings in our patient and propose the PCDH18 gene as a possible candidate gene for intellectual disability.
Collapse
Affiliation(s)
- Jurate Kasnauskiene
- Department of Human and Medical Genetics, Vilnius University, LT-08661 Vilnius, Lithuania.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
307
|
Arlt MF, Wilson TE, Glover TW. Replication stress and mechanisms of CNV formation. Curr Opin Genet Dev 2012; 22:204-10. [PMID: 22365495 DOI: 10.1016/j.gde.2012.01.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 01/24/2012] [Accepted: 01/25/2012] [Indexed: 12/11/2022]
Abstract
Copy number variants (CNVs) are widely distributed throughout the human genome, where they contribute to genetic variation and phenotypic diversity. De novo CNVs are also a major cause of numerous genetic and developmental disorders. However, unlike many other types of mutations, little is known about the genetic and environmental risk factors for new and deleterious CNVs. DNA replication errors have been implicated in the generation of a major class of CNVs, the nonrecurrent CNVs. We have found that agents that perturb normal replication and create conditions of replication stress, including hydroxyurea and aphidicolin, are potent inducers of nonrecurrent CNVs in cultured human cells. These findings have broad implications for identifying CNV risk factors and for hydroxyurea-related therapies in humans.
Collapse
Affiliation(s)
- Martin F Arlt
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, United States
| | | | | |
Collapse
|
308
|
Affiliation(s)
- Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA.
| | | | | |
Collapse
|
309
|
Depienne C, Brice A. Unlocking the genetics of paroxysmal kinesigenic dyskinesia. Brain 2012; 134:3431-4. [PMID: 22171352 DOI: 10.1093/brain/awr319] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
310
|
Costain G, Bassett AS. Clinical applications of schizophrenia genetics: genetic diagnosis, risk, and counseling in the molecular era. APPLICATION OF CLINICAL GENETICS 2012; 5:1-18. [PMID: 23144566 PMCID: PMC3492098 DOI: 10.2147/tacg.s21953] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Schizophrenia is a complex neuropsychiatric disease with documented clinical and genetic heterogeneity, and evidence for neurodevelopmental origins. Driven by new genetic technologies and advances in molecular medicine, there has recently been concrete progress in understanding some of the specific genetic causes of this serious psychiatric illness. In particular, several large rare structural variants have been convincingly associated with schizophrenia, in targeted studies over two decades with respect to 22q11.2 microdeletions, and more recently in large-scale, genome-wide case-control studies. These advances promise to help many families afflicted with this disease. In this review, we critically appraise recent developments in the field of schizophrenia genetics through the lens of immediate clinical applicability. Much work remains in translating the recent surge of genetic research discoveries into the clinic. The epidemiology and basic genetic parameters (such as penetrance and expression) of most genomic disorders associated with schizophrenia are not yet well characterized. To date, 22q11.2 deletion syndrome is the only established genetic subtype of schizophrenia of proven clinical relevance. We use this well-established association as a model to chart the pathway for translating emerging genetic discoveries into clinical practice. We also propose new directions for research involving general genetic risk prediction and counseling in schizophrenia.
Collapse
Affiliation(s)
- Gregory Costain
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, University of Toronto, Toronto, Ontario, Canada ; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | | |
Collapse
|
311
|
Tabet AC, Pilorge M, Delorme R, Amsellem F, Pinard JM, Leboyer M, Verloes A, Benzacken B, Betancur C. Autism multiplex family with 16p11.2p12.2 microduplication syndrome in monozygotic twins and distal 16p11.2 deletion in their brother. Eur J Hum Genet 2012; 20:540-6. [PMID: 22234155 DOI: 10.1038/ejhg.2011.244] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The pericentromeric region of chromosome 16p is rich in segmental duplications that predispose to rearrangements through non-allelic homologous recombination. Several recurrent copy number variations have been described recently in chromosome 16p. 16p11.2 rearrangements (29.5-30.1 Mb) are associated with autism, intellectual disability (ID) and other neurodevelopmental disorders. Another recognizable but less common microdeletion syndrome in 16p11.2p12.2 (21.4 to 28.5-30.1 Mb) has been described in six individuals with ID, whereas apparently reciprocal duplications, studied by standard cytogenetic and fluorescence in situ hybridization techniques, have been reported in three patients with autism spectrum disorders. Here, we report a multiplex family with three boys affected with autism, including two monozygotic twins carrying a de novo 16p11.2p12.2 duplication of 8.95 Mb (21.28-30.23 Mb) characterized by single-nucleotide polymorphism array, encompassing both the 16p11.2 and 16p11.2p12.2 regions. The twins exhibited autism, severe ID, and dysmorphic features, including a triangular face, deep-set eyes, large and prominent nasal bridge, and tall, slender build. The eldest brother presented with autism, mild ID, early-onset obesity and normal craniofacial features, and carried a smaller, overlapping 16p11.2 microdeletion of 847 kb (28.40-29.25 Mb), inherited from his apparently healthy father. Recurrent deletions in this region encompassing the SH2B1 gene were recently reported in early-onset obesity and in individuals with neurodevelopmental disorders associated with phenotypic variability. We discuss the clinical and genetic implications of two different 16p chromosomal rearrangements in this family, and suggest that the 16p11.2 deletion in the father predisposed to the formation of the duplication in his twin children.
Collapse
Affiliation(s)
- Anne-Claude Tabet
- AP-HP, Robert Debré Hospital, Department of Genetics, Cytogenetics Unit, Paris, France
| | | | | | | | | | | | | | | | | |
Collapse
|
312
|
Pehlivan D, Hullings M, Carvalho CMB, Gonzaga-Jauregui CG, Loy E, Jackson LG, Krantz ID, Deardorff MA, Lupski JR. NIPBL rearrangements in Cornelia de Lange syndrome: evidence for replicative mechanism and genotype-phenotype correlation. Genet Med 2012; 14:313-22. [PMID: 22241092 DOI: 10.1038/gim.2011.13] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
PURPOSE Cornelia de Lange syndrome (CdLS) is a multisystem congenital anomaly disorder characterized by mental retardation, limb abnormalities, distinctive facial features, and hirsutism. Mutations in three genes involved in sister chromatid cohesion, NIPBL, SMC1A, and SMC3, account for ~55% of CdLS cases. The molecular etiology of a significant fraction of CdLS cases remains unknown. We hypothesized that large genomic rearrangements of cohesin complex subunit genes may play a role in the molecular etiology of this disorder. METHODS Custom high-resolution oligonucleotide array comparative genomic hybridization analyses interrogating candidate cohesin genes and breakpoint junction sequencing of identified genomic variants were performed. RESULTS Of the 162 patients with CdLS, for whom mutations in known CdLS genes were previously negative by sequencing, deletions containing NIPBL exons were observed in 7 subjects (~5%). Breakpoint sequences in five patients implicated microhomology-mediated replicative mechanisms-such as serial replication slippage and fork stalling and template switching/microhomology-mediated break-induced replication-as a potential predominant contributor to these copy number variations. Most deletions are predicted to result in haploinsufficiency due to heterozygous loss-of-function mutations; such mutations may result in a more severe CdLS phenotype. CONCLUSION Our findings suggest a potential clinical utility to testing for copy number variations involving NIPBL when clinically diagnosed CdLS cases are mutation-negative by DNA-sequencing studies.
Collapse
Affiliation(s)
- Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
313
|
Abstract
During the past decade, widespread use of microarray-based technologies, including oligonucleotide array comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) genotyping arrays have dramatically changed our perspective on genome-wide structural variation. Submicroscopic genomic rearrangements or copy-number variation (CNV) have proven to be an important factor responsible for primate evolution, phenotypic differences between individuals and populations, and susceptibility to many diseases. The number of diseases caused by chromosomal microdeletions and microduplications, also referred to as genomic disorders, has been increasing at a rapid pace. Microdeletions and microduplications are found in patients with a wide variety of phenotypes, including Mendelian diseases as well as common complex traits, such as developmental delay/intellectual disability, autism, schizophrenia, obesity, and epilepsy. This chapter provides an overview of common microdeletion and microduplication syndromes and their clinical phenotypes, and discusses the genomic structures and molecular mechanisms of formation. In addition, an explanation for how these genomic rearrangements convey abnormal phenotypes is provided.
Collapse
Affiliation(s)
- Lisenka E L M Vissers
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | | |
Collapse
|
314
|
D'Angelo CS, Koiffmann CP. Copy number variants in obesity-related syndromes: review and perspectives on novel molecular approaches. J Obes 2012; 2012:845480. [PMID: 23316347 PMCID: PMC3534325 DOI: 10.1155/2012/845480] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/09/2012] [Indexed: 02/07/2023] Open
Abstract
In recent decades, obesity has reached epidemic proportions worldwide and became a major concern in public health. Despite heritability estimates of 40 to 70% and the long-recognized genetic basis of obesity in a number of rare cases, the list of common obesity susceptibility variants by the currently published genome-wide association studies (GWASs) only explain a small proportion of the individual variation in risk of obesity. It was not until very recently that GWASs of copy number variants (CNVs) in individuals with extreme phenotypes reported a number of large and rare CNVs conferring high risk to obesity, and specifically deletions on chromosome 16p11.2. In this paper, we comment on the recent advances in the field of genetics of obesity with an emphasis on the genes and genomic regions implicated in highly penetrant forms of obesity associated with developmental disorders. Array genomic hybridization in this patient population has afforded discovery opportunities for CNVs that have not previously been detectable. This information can be used to generate new diagnostic arrays and sequencing platforms, which will likely enhance detection of known genetic conditions with the potential to elucidate new disease genes and ultimately help in developing a next-generation sequencing protocol relevant to clinical practice.
Collapse
Affiliation(s)
- Carla Sustek D'Angelo
- Human Genome and Stem Cell Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, 277 Rua do Matao, Rooms 204 and 209, 05508-090 Sao Paulo, SP, Brazil.
| | | |
Collapse
|
315
|
Arguello PA, Gogos JA. Genetic and cognitive windows into circuit mechanisms of psychiatric disease. Trends Neurosci 2012; 35:3-13. [PMID: 22177981 DOI: 10.1016/j.tins.2011.11.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 10/26/2011] [Accepted: 11/18/2011] [Indexed: 01/12/2023]
Affiliation(s)
- P Alexander Arguello
- Princeton Neuroscience Institute and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | | |
Collapse
|
316
|
Melhem N, Middleton F, McFadden K, Klei L, Faraone SV, Vinogradov S, Tiobech J, Yano V, Kuartei S, Roeder K, Byerley W, Devlin B, Myles-Worsley M. Copy number variants for schizophrenia and related psychotic disorders in Oceanic Palau: risk and transmission in extended pedigrees. Biol Psychiatry 2011; 70:1115-21. [PMID: 21982423 PMCID: PMC3224197 DOI: 10.1016/j.biopsych.2011.08.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 07/08/2011] [Accepted: 08/02/2011] [Indexed: 12/31/2022]
Abstract
BACKGROUND We report on copy number variants (CNVs) found in Palauan subjects ascertained for schizophrenia and related psychotic disorders in extended pedigrees in Palau. We compare CNVs found in this Oceanic population with those seen in other samples, typically of European ancestry. Assessing CNVs in Palauan extended pedigrees yields insight into the evolution of risk CNVs, such as how they arise, are transmitted, and are lost from populations by stochastic or selective processes, none of which are easily measured from case-control samples. METHODS DNA samples from 197 subjects affected with schizophrenia and related psychotic disorders, 185 of their relatives, and 159 control subjects were successfully characterized for CNVs using Affymetrix Genomewide Human SNP Array 5.0. RESULTS Copy number variants thought to be associated with risk for schizophrenia and related disorders also occur in affected individuals in Palau, specifically 15q11.2 and 1q21.1 deletions, partial duplication of IL1RAPL1 (Xp21.3), and chromosome X duplications (Klinefelter's syndrome). Partial duplication within A2BP1 appears to convey an eightfold increased risk in male subjects (95% confidence interval, .8-84.4) but not female subjects (odds ratio = .4, 95% confidence interval, .03-4.9). Affected-only linkage analysis using this variant yields a logarithm of the odds score of 3.5. CONCLUSIONS This study reveals CNVs that confer risk to schizophrenia and related psychotic disorders in Palau, most of which have been previously observed in samples of European ancestry. Only a few of these CNVs show evidence that they have existed for many generations, consistent with risk variants diminishing reproductive success.
Collapse
Affiliation(s)
- Nadine Melhem
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Frank Middleton
- Department of Psychiatry, SUNY Upstate Medical University; Syracuse NY
| | - Kathryn McFadden
- Division of Neuropathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Stephen V Faraone
- Department of Psychiatry, SUNY Upstate Medical University; Syracuse NY
| | - Sophia Vinogradov
- Department of Psychiatry, University of California San Francisco, Pittsburgh, PA
| | - Josepha Tiobech
- Palauan Ministry of Health, Republic of Palau, Pittsburgh, PA
| | - Victor Yano
- Palauan Ministry of Health, Republic of Palau, Pittsburgh, PA
| | | | - Kathryn Roeder
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA
| | - William Byerley
- Department of Psychiatry, University of California San Francisco, Pittsburgh, PA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | |
Collapse
|
317
|
Mefford HC, Yendle SC, Hsu C, Cook J, Geraghty E, McMahon JM, Eeg-Olofsson O, Sadleir LG, Gill D, Ben-Zeev B, Lerman-Sagie T, Mackay M, Freeman JL, Andermann E, Pelakanos JT, Andrews I, Wallace G, Eichler EE, Berkovic SF, Scheffer IE. Rare copy number variants are an important cause of epileptic encephalopathies. Ann Neurol 2011; 70:974-85. [PMID: 22190369 PMCID: PMC3245646 DOI: 10.1002/ana.22645] [Citation(s) in RCA: 179] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Rare copy number variants (CNVs)--deletions and duplications--have recently been established as important risk factors for both generalized and focal epilepsies. A systematic assessment of the role of CNVs in epileptic encephalopathies, the most devastating and often etiologically obscure group of epilepsies, has not been performed. METHODS We evaluated 315 patients with epileptic encephalopathies characterized by epilepsy and progressive cognitive impairment for rare CNVs using a high-density, exon-focused, whole-genome oligonucleotide array. RESULTS We found that 25 of 315 (7.9%) of our patients carried rare CNVs that may contribute to their phenotype, with at least one-half being clearly or likely pathogenic. We identified 2 patients with overlapping deletions at 7q21 and 2 patients with identical duplications of 16p11.2. In our cohort, large deletions were enriched in affected individuals compared to controls, and 4 patients harbored 2 rare CNVs. We screened 2 novel candidate genes found within the rare CNVs in our cohort but found no mutations in our patients with epileptic encephalopathies. We highlight several additional novel candidate genes located in CNV regions. INTERPRETATION Our data highlight the significance of rare CNVs in the epileptic encephalopathies, and we suggest that CNV analysis should be considered in the genetic evaluation of these patients. Our findings also highlight novel candidate genes for further study.
Collapse
Affiliation(s)
- Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
318
|
McGrew SG, Peters BR, Crittendon JA, Veenstra-VanderWeele J. Diagnostic Yield of Chromosomal Microarray Analysis in an Autism Primary Care Practice: Which Guidelines to Implement? J Autism Dev Disord 2011; 42:1582-91. [DOI: 10.1007/s10803-011-1398-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
319
|
Schaaf CP, Wiszniewska J, Beaudet AL. Copy number and SNP arrays in clinical diagnostics. Annu Rev Genomics Hum Genet 2011; 12:25-51. [PMID: 21801020 DOI: 10.1146/annurev-genom-092010-110715] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The ability of chromosome microarray analysis (CMA) to detect submicroscopic genetic abnormalities has revolutionized the clinical diagnostic approach to individuals with intellectual disability, neurobehavioral phenotypes, and congenital malformations. The recognition of the underlying copy number variant (CNV) in respective individuals may allow not only for better counseling and anticipatory guidance but also for more specific therapeutic interventions in some cases. The use of CMA technology in prenatal diagnosis is emerging and promises higher sensitivity for several highly penetrant, clinically severe microdeletion and microduplication syndromes. Genetic counseling complements the diagnostic testing with CMA, given the presence of CNVs of uncertain clinical significance, incomplete penetrance, and variable expressivity in some cases. While oligonucleotide arrays with high-density exonic coverage remain the gold standard for the detection of CNVs, single-nucleotide polymorphism (SNP) arrays allow for detection of consanguinity and most cases of uniparental disomy and provide a higher sensitivity to detect low-level mosaic aneuploidies.
Collapse
Affiliation(s)
- Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | |
Collapse
|
320
|
Dosage-dependent phenotypes in models of 16p11.2 lesions found in autism. Proc Natl Acad Sci U S A 2011; 108:17076-81. [PMID: 21969575 DOI: 10.1073/pnas.1114042108] [Citation(s) in RCA: 220] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Recurrent copy number variations (CNVs) of human 16p11.2 have been associated with a variety of developmental/neurocognitive syndromes. In particular, deletion of 16p11.2 is found in patients with autism, developmental delay, and obesity. Patients with deletions or duplications have a wide range of clinical features, and siblings carrying the same deletion often have diverse symptoms. To study the consequence of 16p11.2 CNVs in a systematic manner, we used chromosome engineering to generate mice harboring deletion of the chromosomal region corresponding to 16p11.2, as well as mice harboring the reciprocal duplication. These 16p11.2 CNV models have dosage-dependent changes in gene expression, viability, brain architecture, and behavior. For each phenotype, the consequence of the deletion is more severe than that of the duplication. Of particular note is that half of the 16p11.2 deletion mice die postnatally; those that survive to adulthood are healthy and fertile, but have alterations in the hypothalamus and exhibit a "behavior trap" phenotype-a specific behavior characteristic of rodents with lateral hypothalamic and nigrostriatal lesions. These findings indicate that 16p11.2 CNVs cause brain and behavioral anomalies, providing insight into human neurodevelopmental disorders.
Collapse
|
321
|
Lupski JR, Belmont JW, Boerwinkle E, Gibbs RA. Clan genomics and the complex architecture of human disease. Cell 2011; 147:32-43. [PMID: 21962505 PMCID: PMC3656718 DOI: 10.1016/j.cell.2011.09.008] [Citation(s) in RCA: 261] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 09/07/2011] [Accepted: 09/09/2011] [Indexed: 01/12/2023]
Abstract
Human diseases are caused by alleles that encompass the full range of variant types, from single-nucleotide changes to copy-number variants, and these variations span a broad frequency spectrum, from the very rare to the common. The picture emerging from analysis of whole-genome sequences, the 1000 Genomes Project pilot studies, and targeted genomic sequencing derived from very large sample sizes reveals an abundance of rare and private variants. One implication of this realization is that recent mutation may have a greater influence on disease susceptibility or protection than is conferred by variations that arose in distant ancestors.
Collapse
Affiliation(s)
- James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, University of Texas Health Science Center at Houston, Houston, TX 77030-1501, USA
| | - John W. Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030-1501, USA
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
322
|
Gejman PV, Sanders AR, Kendler KS. Genetics of Schizophrenia: New Findings and Challenges. Annu Rev Genomics Hum Genet 2011; 12:121-44. [DOI: 10.1146/annurev-genom-082410-101459] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Pablo V. Gejman
- Center for Psychiatric Genetics, NorthShore University HealthSystem Research Institute, and University of Chicago, Evanston, Illinois 60201;
| | - Alan R. Sanders
- Center for Psychiatric Genetics, NorthShore University HealthSystem Research Institute, and University of Chicago, Evanston, Illinois 60201;
| | - Kenneth S. Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics and Departments of Psychiatry and Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298;
| |
Collapse
|
323
|
Mental retardation and autism associated with recurrent 16p11.2 microdeletion: incomplete penetrance and variable expressivity. J Appl Genet 2011; 52:443-9. [PMID: 21931978 DOI: 10.1007/s13353-011-0063-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 09/02/2011] [Accepted: 09/02/2011] [Indexed: 10/17/2022]
|
324
|
Abstract
Characterized by a combination of abnormalities in language, social cognition and mental flexibility, autism is not a single disorder but a neurodevelopmental syndrome commonly referred to as autism spectrum disorder (ASD). Several dozen ASD susceptibility genes have been identified in the past decade, collectively accounting for 10-20% of ASD cases. These findings, although demonstrating that ASD is etiologically heterogeneous, provide important clues about its pathophysiology. Diverse genetic and genomic approaches provide evidence converging on disruption of key biological pathways, many of which are also implicated in other allied neurodevelopmental disorders. Knowing the genes involved in ASD provides us with a crucial tool to probe both the specificity of ASD and the shared neurobiological and cognitive features across what are considered clinically distinct disorders, with the goal of linking gene to brain circuits to cognitive function.
Collapse
Affiliation(s)
- Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
| |
Collapse
|
325
|
|
326
|
Jacquemont S, Reymond A, Zufferey F, Harewood L, Walters RG, Kutalik Z, Martinet D, Shen Y, Valsesia A, Beckmann ND, Thorleifsson G, Belfiore M, Bouquillon S, Campion D, De Leeuw N, De Vries BBA, Esko T, Fernandez BA, Fernández-Aranda F, Fernández-Real JM, Gratacòs M, Guilmatre A, Hoyer J, Jarvelin MR, Kooy FR, Kurg A, Le Caignec C, Männik K, Platt OS, Sanlaville D, Van Haelst MM, Villatoro Gomez S, Walha F, Wu BL, Yu Y, Aboura A, Addor MC, Alembik Y, Antonarakis SE, Arveiler B, Barth M, Bednarek N, Béna F, Bergmann S, Beri M, Bernardini L, Blaumeiser B, Bonneau D, Bottani A, Boute O, Brunner HG, Cailley D, Callier P, Chiesa J, Chrast J, Coin L, Coutton C, Cuisset JM, Cuvellier JC, David A, De Freminville B, Delobel B, Delrue MA, Demeer B, Descamps D, Didelot G, Dieterich K, Disciglio V, Doco-Fenzy M, Drunat S, Duban-Bedu B, Dubourg C, El-Sayed Moustafa JS, Elliott P, Faas BHW, Faivre L, Faudet A, Fellmann F, Ferrarini A, Fisher R, Flori E, Forer L, Gaillard D, Gerard M, Gieger C, Gimelli S, Gimelli G, Grabe HJ, Guichet A, Guillin O, Hartikainen AL, Heron D, Hippolyte L, Holder M, Homuth G, Isidor B, Jaillard S, Jaros Z, Jiménez-Murcia S, Joly Helas G, Jonveaux P, Kaksonen S, Keren B, Kloss-Brandstätter A, Knoers NVAM, Koolen DA, Kroisel PM, Kronenberg F, Labalme A, Landais E, Lapi E, Layet V, Legallic S, Leheup B, Leube B, Lewis S, Lucas J, Macdermot KD, Magnusson P, Marshall CR, Mathieu-Dramard M, Mccarthy MI, Meitinger T, Antonietta Mencarelli M, Merla G, Moerman A, Mooser V, Morice-Picard F, Mucciolo M, Nauck M, Coumba Ndiaye N, Nordgren A, Pasquier L, Petit F, Pfundt R, Plessis G, Rajcan-Separovic E, Paolo Ramelli G, Rauch A, Ravazzolo R, Reis A, Renieri A, Richart C, Ried JS, Rieubland C, Roberts W, Roetzer KM, Rooryck C, Rossi M, Saemundsen E, Satre V, Schurmann C, Sigurdsson E, Stavropoulos DJ, Stefansson H, Tengström C, Thorsteinsdóttir U, Tinahones FJ, Touraine R, Vallée L, Van Binsbergen E, Van Der Aa N, Vincent-Delorme C, Visvikis-Siest S, Vollenweider P, Völzke H, Vulto-Van Silfhout AT, Waeber G, Wallgren-Pettersson C, Witwicki RM, Zwolinksi S, Andrieux J, Estivill X, Gusella JF, Gustafsson O, Metspalu A, Scherer SW, Stefansson K, Blakemore AIF, Beckmann JS, Froguel P. Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus. Nature 2011; 478:97-102. [PMID: 21881559 PMCID: PMC3637175 DOI: 10.1038/nature10406] [Citation(s) in RCA: 309] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 07/29/2011] [Indexed: 12/25/2022]
Abstract
Both obesity and being underweight have been associated with increased mortality. Underweight, defined as a body mass index (BMI) ≤ 18.5 kg per m(2) in adults and ≤ -2 standard deviations from the mean in children, is the main sign of a series of heterogeneous clinical conditions including failure to thrive, feeding and eating disorder and/or anorexia nervosa. In contrast to obesity, few genetic variants underlying these clinical conditions have been reported. We previously showed that hemizygosity of a ∼600-kilobase (kb) region on the short arm of chromosome 16 causes a highly penetrant form of obesity that is often associated with hyperphagia and intellectual disabilities. Here we show that the corresponding reciprocal duplication is associated with being underweight. We identified 138 duplication carriers (including 132 novel cases and 108 unrelated carriers) from individuals clinically referred for developmental or intellectual disabilities (DD/ID) or psychiatric disorders, or recruited from population-based cohorts. These carriers show significantly reduced postnatal weight and BMI. Half of the boys younger than five years are underweight with a probable diagnosis of failure to thrive, whereas adult duplication carriers have an 8.3-fold increased risk of being clinically underweight. We observe a trend towards increased severity in males, as well as a depletion of male carriers among non-medically ascertained cases. These features are associated with an unusually high frequency of selective and restrictive eating behaviours and a significant reduction in head circumference. Each of the observed phenotypes is the converse of one reported in carriers of deletions at this locus. The phenotypes correlate with changes in transcript levels for genes mapping within the duplication but not in flanking regions. The reciprocal impact of these 16p11.2 copy-number variants indicates that severe obesity and being underweight could have mirror aetiologies, possibly through contrasting effects on energy balance.
Collapse
Affiliation(s)
| | - Alexandre Reymond
- Centre de génomique intégrative
Université de Lausanne1015 Lausanne,CH
| | - Flore Zufferey
- Service de génétique médicale
CHU Vaudois1011 Lausanne,CH
| | - Louise Harewood
- Centre de génomique intégrative
Université de Lausanne1015 Lausanne,CH
| | - Robin G. Walters
- Department of Genomics of Common Disease
Imperial College LondonHammersmith hospital, London W12 0NN,GB
| | - Zoltán Kutalik
- Department of Medical Genetics
University of LausanneCH
- SIB, Swiss Institute of Bioinformatics
Swiss Institute of BioinformaticsQuartier Sorge - Batiment Genopode 1015 Lausanne Switzerland,CH
| | | | - Yiping Shen
- Laboratory Medicine
Children's Hospital BostonBoston, Massachusetts 02115,US
- Center for Human Genetic Research
Massachusetts General HospitalBoston, Massachusetts 02114,US
| | - Armand Valsesia
- Department of Medical Genetics
University of LausanneCH
- SIB, Swiss Institute of Bioinformatics
Swiss Institute of BioinformaticsQuartier Sorge - Batiment Genopode 1015 Lausanne Switzerland,CH
- Ludwig Institute for Cancer Research
Université de Lausanne1015 Lausanne,CH
| | | | | | - Marco Belfiore
- Service de génétique médicale
CHU Vaudois1011 Lausanne,CH
| | - Sonia Bouquillon
- Laboratoire de Génétique Médicale
Hôpital Jeanne de FlandreCHRU Lille59037 Lille Cedex,FR
| | - Dominique Campion
- Génétique médicale et fonctionnelle du cancer et des maladies neuropsychiatriques
INSERM : U614Université de RouenUFR de Medecine et de Pharmacie 22, Boulevard Gambetta 76183 Rouen cedex,FR
- Estonian Genome and Medicine
University of Tartu51010 Tartu,EE
| | - Nicole De Leeuw
- Department of human genetics
Radboud University Nijmegen Medical CentreNijmegen Centre for Molecular Life SciencesInstitute for Genetic and Metabolic Disorders6500 HB Nijmegen,NL
| | - Bert B. A. De Vries
- Department of human genetics
Radboud University Nijmegen Medical CentreNijmegen Centre for Molecular Life SciencesInstitute for Genetic and Metabolic Disorders6500 HB Nijmegen,NL
| | - Tõnu Esko
- Estonian Genome and Medicine
University of Tartu51010 Tartu,EE
- Institute of Molecular and Cell Biology
University of Tartu51010 Tartu,EE
| | - Bridget A. Fernandez
- Disciplines of Genetics and Medicine
Memorial University of NewfoundlandSt. John's Newfoundland,CA
| | - Fernando Fernández-Aranda
- IDIBELL, Department of Psychiatry
University Hospital of BellvitgeCIBERobn Fisiopatología de la Obesidad y Nutrición08907 Barcelona,ES
| | - José Manuel Fernández-Real
- Section of Diabetes, Endocrinology and Nutrition
University Hospital of GironaBiomedical Research Institute "Dr Josep Trueta"CIBERobn Fisiopatología de la Obesidad y Nutrición17007 Girona,ES
| | - Mònica Gratacòs
- CRG-UPF, Center for Genomic Regulation
CIBER de Epidemiología y Salud Pública (CIBERESP)C/ Dr. Aiguader, 88 08003 Barcelona, Catalonia, Spain,ES
| | - Audrey Guilmatre
- Génétique médicale et fonctionnelle du cancer et des maladies neuropsychiatriques
INSERM : U614Université de RouenUFR de Medecine et de Pharmacie 22, Boulevard Gambetta 76183 Rouen cedex,FR
- Estonian Genome and Medicine
University of Tartu51010 Tartu,EE
| | - Juliane Hoyer
- Institute of Human Genetics
Friedrich-Alexander University Erlangen-Nuremberg91054 Erlangen,DE
| | - Marjo-Riitta Jarvelin
- Department of child and adolescent health
National Institute for Health and WelfareUniversity of OuluInstitute of Health Sciences and Biocenter OuluBox 310, 90101 Oulu,FI
| | - Frank R. Kooy
- Department of Medical Genetics
University Hospital Antwerp2650 Edegem,BE
| | - Ants Kurg
- Institute of Molecular and Cell Biology
University of Tartu51010 Tartu,EE
| | - Cédric Le Caignec
- Service d'ORL et de Chirurgie Cervicofaciale
INSERM : U587Hôpital d'Enfants Armand-TrousseauUniversité Pierre et Marie Curie - Paris 6Paris,FR
| | - Katrin Männik
- Institute of Molecular and Cell Biology
University of Tartu51010 Tartu,EE
| | - Orah S. Platt
- Laboratory Medicine
Children's Hospital BostonBoston, Massachusetts 02115,US
| | - Damien Sanlaville
- Service de cytogénétique constitutionnelle
Hospices Civils de LyonCHU de LyonCentre Neuroscience et Recherche69000 Lyon,FR
| | - Mieke M. Van Haelst
- Department of Genomics of Common Disease
Imperial College LondonHammersmith hospital, London W12 0NN,GB
- Department of Medical Genetics
University Medical Center Utrecht3584 EA Utrecht,NL
| | - Sergi Villatoro Gomez
- CRG-UPF, Center for Genomic Regulation
CIBER de Epidemiología y Salud Pública (CIBERESP)C/ Dr. Aiguader, 88 08003 Barcelona, Catalonia, Spain,ES
| | - Faida Walha
- Centre de génomique intégrative
Université de Lausanne1015 Lausanne,CH
| | - Bai-Lin Wu
- Laboratory Medicine
Children's Hospital BostonBoston, Massachusetts 02115,US
- Institutes of Biomedical Science
Fudan UniversityChildren's Hospital200032 Shanghai,CN
| | - Yongguo Yu
- Laboratory Medicine
Children's Hospital BostonBoston, Massachusetts 02115,US
- Shanghai Children's Medical Center
Shanghai Children's Medical Center200127 Shanghai,CN
| | - Azzedine Aboura
- Département de génétique
Assistance publique - Hôpitaux de Paris (AP-HP)Hôpital Robert DebréUniversité Paris VII - Paris Diderot48, boulevard Sérurier 75935 Paris cedex 19,FR
| | | | - Yves Alembik
- Service de cytogénétique
CHU StrasbourgHôpital de Hautepierre1 Av Moliere 67098 Strasbourg Cedex,FR
| | | | - Benoît Arveiler
- MRGM, Maladies Rares - Génétique et Métabolisme
Hôpital PellegrinService de Génétique Médicale du CHU de BordeauxUniversité Victor Segalen - Bordeaux II : EA4576146 rue Léo-Saignat - 33076 Bordeaux Cedex,FR
- Service de génétique médicale
CHU BordeauxGroupe hospitalier PellegrinUniversité de BordeauxBordeaux,FR
| | - Magalie Barth
- Service de génétique [Angers]
CHU AngersUniversité d'Angersrue Larrey, 49100 Angers,FR
| | - Nathalie Bednarek
- URCA, Université de Reims Champagne-Ardenne
Ministère de l'Enseignement Supérieur et de la Recherche Scientifique9 boulevard Paix - 51097 Reims cedex,FR
| | - Frédérique Béna
- Génétique médicale
Hôpitaux Universitaires de Genève1205 Geneva,CH
| | - Sven Bergmann
- Department of Medical Genetics
University of LausanneCH
- SIB, Swiss Institute of Bioinformatics
Swiss Institute of BioinformaticsQuartier Sorge - Batiment Genopode 1015 Lausanne Switzerland,CH
- Department of Molecular Genetics
Weizmann Institute of ScienceRehovot,IL
| | - Mylène Beri
- Laboratoire de Génétique
CHU NancyVandoeuvre les Nancy,FR
| | - Laura Bernardini
- Mendel Laboratory
IRCCS Casa Sollievo della Sofferenza Hospital71013 San Giovanni Rotondo,IT
| | - Bettina Blaumeiser
- Department of Medical Genetics
University Hospital Antwerp2650 Edegem,BE
| | - Dominique Bonneau
- Service de génétique [Angers]
CHU AngersUniversité d'Angersrue Larrey, 49100 Angers,FR
| | - Armand Bottani
- Génétique médicale
Hôpitaux Universitaires de Genève1205 Geneva,CH
| | - Odile Boute
- Service de Génétique clinique
Hôpital Jeanne de FlandreCHRU Lille2 avenue Oscar Lambret, 59000 Lille,FR
| | - Han G. Brunner
- Department of human genetics
Radboud University Nijmegen Medical CentreNijmegen Centre for Molecular Life SciencesInstitute for Genetic and Metabolic Disorders6500 HB Nijmegen,NL
| | - Dorothée Cailley
- Service de génétique médicale
CHU BordeauxGroupe hospitalier PellegrinUniversité de BordeauxBordeaux,FR
| | | | - Jean Chiesa
- Laboratoire de Cytogénétique
CHU Nîmes30029 Nimes,FR
| | - Jacqueline Chrast
- Centre de génomique intégrative
Université de Lausanne1015 Lausanne,CH
| | - Lachlan Coin
- Department of Genomics of Common Disease
Imperial College LondonHammersmith hospital, London W12 0NN,GB
| | - Charles Coutton
- Département de génétique et procréation
CHU GrenobleUniversité Joseph Fourier - Grenoble Ifaculté de médecine-pharmacieDomaine de la Merci, 38706 Grenoble,FR
- AGIM, AGeing and IMagery, CNRS FRE3405
Université Joseph Fourier - Grenoble IEcole Pratique des Hautes EtudesCNRS : UMR5525Faculté de médecine de Grenoble, 38700 La Tronche,FR
- Laboratoire de biochimie et génétique moléculaire
CHU Grenoble38043 Grenoble,FR
| | - Jean-Marie Cuisset
- Service de Neuropédiatrie
CHRU LilleHôpital Roger Salengro59037 Lille,FR
| | | | - Albert David
- Service d'ORL et de Chirurgie Cervicofaciale
INSERM : U587Hôpital d'Enfants Armand-TrousseauUniversité Pierre et Marie Curie - Paris 6Paris,FR
| | | | - Bruno Delobel
- Centre de Génétique Chromosomique
GHICLHôpital Saint Vincent de PaulBoulevard de Belfort B.P. 387 59020 LILLE CEDEX,FR
| | - Marie-Ange Delrue
- MRGM, Maladies Rares - Génétique et Métabolisme
Hôpital PellegrinService de Génétique Médicale du CHU de BordeauxUniversité Victor Segalen - Bordeaux II : EA4576146 rue Léo-Saignat - 33076 Bordeaux Cedex,FR
- Service de génétique médicale
CHU BordeauxGroupe hospitalier PellegrinUniversité de BordeauxBordeaux,FR
| | - Bénédicte Demeer
- Service de génétique médicale
CHU AMIENSPlace Victor Pauchet, 80054 Amiens Cedex 1,FR
| | - Dominique Descamps
- Centre hospitalier de Béthune
Centre hospitalier de Béthune62408 Bethune,FR
| | - Gérard Didelot
- Centre de génomique intégrative
Université de Lausanne1015 Lausanne,CH
| | | | - Vittoria Disciglio
- Department of Biotechnology
Università degli studi di SienaMedical Genetics53100 Siena,IT
| | - Martine Doco-Fenzy
- Service de Génétique
CHU ReimsHôpital Maison BlancheIFR 5351092 Reims,FR
| | - Séverine Drunat
- Département de génétique
Assistance publique - Hôpitaux de Paris (AP-HP)Hôpital Robert DebréUniversité Paris VII - Paris Diderot48, boulevard Sérurier 75935 Paris cedex 19,FR
| | - Bénédicte Duban-Bedu
- Centre de Génétique Chromosomique
GHICLHôpital Saint Vincent de PaulBoulevard de Belfort B.P. 387 59020 LILLE CEDEX,FR
| | - Christèle Dubourg
- IGDR, Institut de Génétique et Développement de Rennes
CNRS : UMR6061Université de Rennes 1IFR140Faculté de Médecine - CS 34317 2 Av du Professeur Léon Bernard 35043 RENNES CEDEX,FR
| | | | - Paul Elliott
- Department of Epidemiology and Public Health
Imperial College LondonSt Mary's Campus, Norfolk Place, London W2 1PG,GB
| | - Brigitte H. W. Faas
- Department of human genetics
Radboud University Nijmegen Medical CentreNijmegen Centre for Molecular Life SciencesInstitute for Genetic and Metabolic Disorders6500 HB Nijmegen,NL
- Department of Human Genetics, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen
Department of Human Genetics, Radboud University Medical Centre, PO Box 9101, 6500 HB NijmegenNL
| | - Laurence Faivre
- Department of Experimental Cardiology
Heart Failure Research Center (HFRC)Academic Medical Center (AMC)Meibergdreef 9, PO Box 22660, 1100 DD Amsterdam,NL
| | - Anne Faudet
- Département de Génétique Cytogénétique et Embryologie
Assistance publique - Hôpitaux de Paris (AP-HP)Hôpital Pitié-SalpêtrièreUniversité Paris VI - Pierre et Marie Curie47-83, boulevard de l'Hôpital 75651 PARIS Cedex 13,FR
| | | | | | - Richard Fisher
- Institute of human genetics
International Centre for LifeNewcastle Upon Tyne NE1 4EP,GB
| | - Elisabeth Flori
- Service de cytogénétique
CHU StrasbourgHôpital de Hautepierre1 Av Moliere 67098 Strasbourg Cedex,FR
| | - Lukas Forer
- Division of genetic epidemiology
Innsbruck Medical UniversityDepartment of Medical GeneticsMolecular and Clinical Pharmacology6020 Innsbruck,AT
| | - Dominique Gaillard
- Service de Génétique
CHU ReimsHôpital Maison BlancheIFR 5351092 Reims,FR
| | - Marion Gerard
- Département de génétique
Assistance publique - Hôpitaux de Paris (AP-HP)Hôpital Robert DebréUniversité Paris VII - Paris Diderot48, boulevard Sérurier 75935 Paris cedex 19,FR
| | - Christian Gieger
- Institute of Experimental Medicine
Academy of Sciences of the Czech RepublicVídeÅ�ská 1083 142 20 Prague,CZ
| | - Stefania Gimelli
- Génétique médicale
Hôpitaux Universitaires de Genève1205 Geneva,CH
- Department of Obstetrics and Gynecology
Institute of Clinical MedicineUniversity of Oulu90570 Oulu,FI
| | - Giorgio Gimelli
- Laboratorio di citogenetica
G. Gaslini Institute16147 Genova,IT
| | - Hans J. Grabe
- Department of Psychiatry and Psychotherapy
Ernst-Moritz-Arndt University Greifswald17475 Greifswald and D-18437 Stralsund,DE
| | - Agnès Guichet
- Service de génétique [Angers]
CHU AngersUniversité d'Angersrue Larrey, 49100 Angers,FR
| | - Olivier Guillin
- Génétique médicale et fonctionnelle du cancer et des maladies neuropsychiatriques
INSERM : U614Université de RouenUFR de Medecine et de Pharmacie 22, Boulevard Gambetta 76183 Rouen cedex,FR
| | - Anna-Liisa Hartikainen
- Department of Obstetrics and Gynecology
Institute of Clinical MedicineUniversity of Oulu90570 Oulu,FI
| | - Délphine Heron
- Département de Génétique Cytogénétique et Embryologie
Assistance publique - Hôpitaux de Paris (AP-HP)Hôpital Pitié-SalpêtrièreUniversité Paris VI - Pierre et Marie Curie47-83, boulevard de l'Hôpital 75651 PARIS Cedex 13,FR
| | | | - Muriel Holder
- Service de Génétique clinique
Hôpital Jeanne de FlandreCHRU Lille2 avenue Oscar Lambret, 59000 Lille,FR
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics
Ernst-Moritz-Arndt University GreifswaldD-17487 Greifswald,DE
| | - Bertrand Isidor
- Service d'ORL et de Chirurgie Cervicofaciale
INSERM : U587Hôpital d'Enfants Armand-TrousseauUniversité Pierre et Marie Curie - Paris 6Paris,FR
| | - Sylvie Jaillard
- IGDR, Institut de Génétique et Développement de Rennes
CNRS : UMR6061Université de Rennes 1IFR140Faculté de Médecine - CS 34317 2 Av du Professeur Léon Bernard 35043 RENNES CEDEX,FR
| | - Zdenek Jaros
- Abteilung für Kinder und Jugendheilkunde
Landesklinikum Waldviertel Zwettl3910 Zwettl,AT
| | - Susana Jiménez-Murcia
- IDIBELL, Department of Psychiatry
University Hospital of BellvitgeCIBERobn Fisiopatología de la Obesidad y Nutrición08907 Barcelona,ES
| | | | | | - Satu Kaksonen
- The Habilitation Unit of Folkhalsan
The Habilitation Unit of FolkhalsanFolkhalsan, SF 00250 Helsinki,FI
| | - Boris Keren
- Département de Génétique Cytogénétique et Embryologie
Assistance publique - Hôpitaux de Paris (AP-HP)Hôpital Pitié-SalpêtrièreUniversité Paris VI - Pierre et Marie Curie47-83, boulevard de l'Hôpital 75651 PARIS Cedex 13,FR
| | - Anita Kloss-Brandstätter
- Division of genetic epidemiology
Innsbruck Medical UniversityDepartment of Medical GeneticsMolecular and Clinical Pharmacology6020 Innsbruck,AT
| | - Nine V. A. M. Knoers
- Department of Medical Genetics
University Medical Center Utrecht3584 EA Utrecht,NL
| | - David A. Koolen
- Department of human genetics
Radboud University Nijmegen Medical CentreNijmegen Centre for Molecular Life SciencesInstitute for Genetic and Metabolic Disorders6500 HB Nijmegen,NL
| | | | - Florian Kronenberg
- Division of genetic epidemiology
Innsbruck Medical UniversityDepartment of Medical GeneticsMolecular and Clinical Pharmacology6020 Innsbruck,AT
| | - Audrey Labalme
- Service de cytogénétique constitutionnelle
Hospices Civils de LyonCHU de LyonCentre Neuroscience et Recherche69000 Lyon,FR
| | - Emilie Landais
- Service de Génétique
CHU ReimsHôpital Maison BlancheIFR 5351092 Reims,FR
| | - Elisabetta Lapi
- Medical Genetics Unit
Children's Hospital Anna Meyer50139 Firenze,IT
| | - Valérie Layet
- Unité de Cytogénétique et Génétique Médicale
Hôpital Gustave FlaubertGroupe Hospitalier du Havre76600 Le Havre,FR
| | - Solenn Legallic
- Génétique médicale et fonctionnelle du cancer et des maladies neuropsychiatriques
INSERM : U614Université de RouenUFR de Medecine et de Pharmacie 22, Boulevard Gambetta 76183 Rouen cedex,FR
| | - Bruno Leheup
- Service de médecine infantile III et génétique clinique
CHU NancyUniversité Henri Poincaré - Nancy IPRES de l'université de Lorraine54511 Vandoeuvre les Nancy,FR
| | - Barbara Leube
- Institute of Human Genetics and Anthropology
Heinrich-Heine University Hospital DuesseldorfD-40001 Duesseldorf,DE
| | - Suzanne Lewis
- Department of Medical Genetics
University of British ColumbiaChild and Family Research InstituteVancouver V6H 3N1,CA
| | - Josette Lucas
- IGDR, Institut de Génétique et Développement de Rennes
CNRS : UMR6061Université de Rennes 1IFR140Faculté de Médecine - CS 34317 2 Av du Professeur Léon Bernard 35043 RENNES CEDEX,FR
| | - Kay D. Macdermot
- North West Thames Regional Genetics Service
Northwick Park & St Marks HospitalHarrow HA1 3UJ,GB
| | - Pall Magnusson
- Child and Adolescent Psychiatry
Landspitali University HospitalIS-105 Reykjavík,IS
| | - Christian R. Marshall
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology
The Hospital for Sick ChildrenToronto, Ontario, M5G 1L7,CA
| | | | - Mark I. Mccarthy
- OCDEM, Oxford Centre for Diabetes, Endocrinology and Metabolism
University of OxfordChurchill Hospital Oxford OX3 7LJ,GB
- Wellcome Trust Centre for Human Genetics
University of OxfordOxford,GB
| | - Thomas Meitinger
- Institute of Human Genetics
HelmholtzZentrum MünchenTechnische Universität München (TUM)German Research Center for Environmental Health85764 Neuherberg,DE
| | | | - Giuseppe Merla
- Medical Genetics Unit
IRCCS Casa Sollievo della Sofferenza Hospital71013 San Giovanni Rotondo,IT
| | - Alexandre Moerman
- Service de Génétique clinique
Hôpital Jeanne de FlandreCHRU Lille2 avenue Oscar Lambret, 59000 Lille,FR
| | - Vincent Mooser
- Genetics, GlaxoSmithKline R&D
GlaxoSmithKline720 Swedeland Road, King of Prussia, Pennsylvania 19406,US
| | - Fanny Morice-Picard
- MRGM, Maladies Rares - Génétique et Métabolisme
Hôpital PellegrinService de Génétique Médicale du CHU de BordeauxUniversité Victor Segalen - Bordeaux II : EA4576146 rue Léo-Saignat - 33076 Bordeaux Cedex,FR
- Service de génétique médicale
CHU BordeauxGroupe hospitalier PellegrinUniversité de BordeauxBordeaux,FR
| | - Mafalda Mucciolo
- Department of Biotechnology
Università degli studi di SienaMedical Genetics53100 Siena,IT
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine
Ernst-Moritz-Arndt University GreifswaldD-17475 Greifswald,DE
| | - Ndeye Coumba Ndiaye
- Génétique cardiovasculaire
Université Henri Poincaré - Nancy I : EA437354000 Nancy,FR
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery
Karolinska InstitutetSE
| | - Laurent Pasquier
- IGDR, Institut de Génétique et Développement de Rennes
CNRS : UMR6061Université de Rennes 1IFR140Faculté de Médecine - CS 34317 2 Av du Professeur Léon Bernard 35043 RENNES CEDEX,FR
| | - Florence Petit
- Service de Génétique clinique
Hôpital Jeanne de FlandreCHRU Lille2 avenue Oscar Lambret, 59000 Lille,FR
| | - Rolph Pfundt
- Department of human genetics
Radboud University Nijmegen Medical CentreNijmegen Centre for Molecular Life SciencesInstitute for Genetic and Metabolic Disorders6500 HB Nijmegen,NL
| | - Ghislaine Plessis
- Service de génétique
CHU CaenHôpital ClémenceauAvenue Georges Clémenceau, Caen,FR
| | - Evica Rajcan-Separovic
- Department of Pathology
University of British ColumbiaChild and Family Research InstituteVancouver, British Columbia V5Z 4H4,CA
| | | | - Anita Rauch
- Institute of Medical Genetics
University of Zurich8603 Schwerzenbach,CH
| | - Roberto Ravazzolo
- Department of pediatrics and CEBR
University of GenovaG. Gaslini Institute16126 Genova,IT
| | - Andre Reis
- Institute of Human Genetics
Friedrich-Alexander University Erlangen-Nuremberg91054 Erlangen,DE
| | - Alessandra Renieri
- Department of Biotechnology
Università degli studi di SienaMedical Genetics53100 Siena,IT
| | - Cristobal Richart
- Department of Internal Medicine
University Hospital Juan XXIIIUniversitat Rovira y VirgiliCiber Fisiopatologia Obesidad y Nutricion (CIBEROBN)Instituto Salud Carlos III43005 Tarragona,ES
| | - Janina S. Ried
- Institute of Experimental Medicine
Academy of Sciences of the Czech RepublicVídeÅ�ská 1083 142 20 Prague,CZ
| | - Claudine Rieubland
- Division of Human Genetics
University of BernDepartment of Paediatrics, Inselspital3010 Bern,CH
| | - Wendy Roberts
- Autism Research Unit
The Hospital for Sick Children and Bloorview Kids RehabilitationUniversity of TorontoToronto, Ontario, M5G 1Z8,CA
| | | | - Caroline Rooryck
- MRGM, Maladies Rares - Génétique et Métabolisme
Hôpital PellegrinService de Génétique Médicale du CHU de BordeauxUniversité Victor Segalen - Bordeaux II : EA4576146 rue Léo-Saignat - 33076 Bordeaux Cedex,FR
- Service de génétique médicale
CHU BordeauxGroupe hospitalier PellegrinUniversité de BordeauxBordeaux,FR
| | - Massimiliano Rossi
- Service de cytogénétique constitutionnelle
Hospices Civils de LyonCHU de LyonCentre Neuroscience et Recherche69000 Lyon,FR
| | | | - Véronique Satre
- Département de génétique et procréation
CHU GrenobleUniversité Joseph Fourier - Grenoble Ifaculté de médecine-pharmacieDomaine de la Merci, 38706 Grenoble,FR
- AGIM, AGeing and IMagery, CNRS FRE3405
Université Joseph Fourier - Grenoble IEcole Pratique des Hautes EtudesCNRS : UMR5525Faculté de médecine de Grenoble, 38700 La Tronche,FR
| | - Claudia Schurmann
- Interfaculty Institute for Genetics and Functional Genomics
Ernst-Moritz-Arndt University GreifswaldD-17487 Greifswald,DE
| | - Engilbert Sigurdsson
- University of Iceland
University of IcelandDepartment of Electrical and Computer Engineering, University of Iceland, Hjardarhaga 2-6, 107 Reykjavik, Iceland;,IS
| | - Dimitri J. Stavropoulos
- Department of Pediatric Laboratory Medicine
Hospital for Sick ChildrenToronto, Ontario M5G 1X8,CA
| | | | - Carola Tengström
- Genetic Services
Rinnekoti Research FoundationKumputie 1, SF-02980 Espoo,FI
| | | | - Francisco J. Tinahones
- Department of Endocrinology and Nutrition
Clinic Hospital of Virgen de la VictoriaCiber Fisiopatologia y Nutricion (CIBEROBN)Instituto Salud Carlos III29010 Malaga,ES
| | - Renaud Touraine
- Service de génétique
CHU Saint-EtienneHôpital nord42055 St Etienne,FR
| | - Louis Vallée
- Service de Neuropédiatrie
CHRU LilleHôpital Roger Salengro59037 Lille,FR
| | - Ellen Van Binsbergen
- Department of Medical Genetics
University Medical Center Utrecht3584 EA Utrecht,NL
| | | | - Catherine Vincent-Delorme
- Centre de Maladies Rares
Anomalies du Développement Nord de FranceCH Arras - CHRU Lille59000 Arras,FR
| | - Sophie Visvikis-Siest
- Génétique cardiovasculaire
Université Henri Poincaré - Nancy I : EA437354000 Nancy,FR
| | - Peter Vollenweider
- Department of Internal Medicine
Centre Hospitalier Universitaire Vaudois1011 Lausanne,CH
| | - Henry Völzke
- Institute for Community Medicine
Ernst-Moritz-Arndt University GreifswaldD-17475 Greifswald,DE
| | - Anneke T. Vulto-Van Silfhout
- Department of human genetics
Radboud University Nijmegen Medical CentreNijmegen Centre for Molecular Life SciencesInstitute for Genetic and Metabolic Disorders6500 HB Nijmegen,NL
| | - Gérard Waeber
- Department of Internal Medicine
Centre Hospitalier Universitaire Vaudois1011 Lausanne,CH
| | - Carina Wallgren-Pettersson
- Department of Medical Genetics
University of HelsinskiFolkhälsan Insitute of GeneticsHaartman Institute00251 Helsinki,FI
| | | | - Simon Zwolinksi
- Institute of human genetics
International Centre for LifeNewcastle Upon Tyne NE1 4EP,GB
| | - Joris Andrieux
- Laboratoire de Génétique Médicale
Hôpital Jeanne de FlandreCHRU Lille59037 Lille Cedex,FR
| | - Xavier Estivill
- CRG-UPF, Center for Genomic Regulation
CIBER de Epidemiología y Salud Pública (CIBERESP)C/ Dr. Aiguader, 88 08003 Barcelona, Catalonia, Spain,ES
| | - James F. Gusella
- Center for Human Genetic Research
Massachusetts General HospitalBoston, Massachusetts 02114,US
| | | | - Andres Metspalu
- Estonian Genome and Medicine
University of Tartu51010 Tartu,EE
- Institute of Molecular and Cell Biology
University of Tartu51010 Tartu,EE
| | - Stephen W. Scherer
- The Centre for Applied Genomics
The Hospital for Sick ChildrenMcLaughlin CentreDepartment of Molecular GeneticsUniversity of TorontoToronto, Ontario, Canada M5G 1L7,CA
| | | | - Alexandra I. F. Blakemore
- Department of Genomics of Common Disease
Imperial College LondonHammersmith hospital, London W12 0NN,GB
| | - Jacques S. Beckmann
- Service de génétique médicale
CHU Vaudois1011 Lausanne,CH
- Department of Medical Genetics
University of LausanneCH
| | - Philippe Froguel
- Department of Genomics of Common Disease
Imperial College LondonHammersmith hospital, London W12 0NN,GB
- IBLI, Institut de biologie de Lille - IBL
Institut Pasteur de LilleCNRS : UMR8090Université Lille I - Sciences et technologiesUniversité Lille II - Droit et santéInstitut de Biologie de Lille 1 Rue du Professeur Calmette - 447 59021 LILLE CEDEX,FR
| |
Collapse
|
327
|
Wat MJ, Veenma D, Hogue J, Holder AM, Yu Z, Wat JJ, Hanchard N, Shchelochkov OA, Fernandes CJ, Johnson A, Lally KP, Slavotinek A, Danhaive O, Schaible T, Cheung SW, Rauen KA, Tonk VS, Tibboel D, de Klein A, Scott DA. Genomic alterations that contribute to the development of isolated and non-isolated congenital diaphragmatic hernia. J Med Genet 2011; 48:299-307. [PMID: 21525063 DOI: 10.1136/jmg.2011.089680] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND Congenital diaphragmatic hernia (CDH) is a life threatening birth defect. Most of the genetic factors that contribute to the development of CDH remain unidentified. OBJECTIVE To identify genomic alterations that contribute to the development of diaphragmatic defects. METHODS A cohort of 45 unrelated patients with CDH or diaphragmatic eventrations was screened for genomic alterations by array comparative genomic hybridisation or single nucleotide polymorphism based copy number analysis. RESULTS Genomic alterations that were likely to have contributed to the development of CDH were identified in 8 patients. Inherited deletions of ZFPM2 were identified in 2 patients with isolated diaphragmatic defects and a large de novo 8q deletion overlapping the same gene was found in a patient with non-isolated CDH. A de novo microdeletion of chromosome 1q41q42 and two de novo microdeletions on chromosome 16p11.2 were identified in patients with non-isolated CDH. Duplications of distal 11q and proximal 13q were found in a patient with non-isolated CDH and a de novo single gene deletion of FZD2 was identified in a patient with a partial pentalogy of Cantrell phenotype. CONCLUSIONS Haploinsufficiency of ZFPM2 can cause dominantly inherited isolated diaphragmatic defects with incomplete penetrance. These data define a new minimal deleted region for CDH on 1q41q42, provide evidence for the existence of CDH related genes on chromosomes 16p11.2, 11q23-24 and 13q12, and suggest a possible role for FZD2 and Wnt signalling in pentalogy of Cantrell phenotypes. These results demonstrate the clinical utility of screening for genomic alterations in individuals with both isolated and non-isolated diaphragmatic defects.
Collapse
Affiliation(s)
- Margaret J Wat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
328
|
Levy D, Ronemus M, Yamrom B, Lee YH, Leotta A, Kendall J, Marks S, Lakshmi B, Pai D, Ye K, Buja A, Krieger A, Yoon S, Troge J, Rodgers L, Iossifov I, Wigler M. Rare de novo and transmitted copy-number variation in autistic spectrum disorders. Neuron 2011; 70:886-97. [PMID: 21658582 DOI: 10.1016/j.neuron.2011.05.015] [Citation(s) in RCA: 497] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2011] [Indexed: 12/01/2022]
Abstract
To explore the genetic contribution to autistic spectrum disorders (ASDs), we have studied genomic copy-number variation in a large cohort of families with a single affected child and at least one unaffected sibling. We confirm a major contribution from de novo deletions and duplications but also find evidence of a role for inherited "ultrarare" duplications. Our results show that, relative to males, females have greater resistance to autism from genetic causes, which raises the question of the fate of female carriers. By analysis of the proportion and number of recurrent loci, we set a lower bound for distinct target loci at several hundred. We find many new candidate regions, adding substantially to the list of potential gene targets, and confirm several loci previously observed. The functions of the genes in the regions of de novo variation point to a great diversity of genetic causes but also suggest functional convergence.
Collapse
Affiliation(s)
- Dan Levy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
329
|
Yu Y, Zhu H, Miller DT, Gusella JF, Platt OS, Wu BL, Shen Y. Age- and gender-dependent obesity in individuals with 16p11.2 deletion. J Genet Genomics 2011; 38:403-9. [PMID: 21930099 DOI: 10.1016/j.jgg.2011.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Revised: 07/29/2011] [Accepted: 08/09/2011] [Indexed: 12/20/2022]
Abstract
Recurrent genomic imbalances at 16p11.2 are genetic risk factors of variable penetrance for developmental delay and autism. Recently, 16p11.2 (chr16:29.5 Mb-30.1 Mb) deletion has also been detected in individuals with early-onset severe obesity. The penetrance of 16p11.2 deletion as a genetic risk factor for obesity is unknown. We evaluated the growth and body mass characteristics of 28 individuals with 16p11.2 (chr16:29.5 Mb-30.1 Mb) deletion originally ascertained for their developmental disorders by reviewing their medical records. We found that nine individuals could be classified as obese and six as overweight. These individuals generally had early feeding and growth difficulties, and started to gain excessive weight around 5-6 years of age. Thirteen out of the 18 deletion carriers aged 5 years and older (72%) were overweight or obese, whereas only two of 10 deletion carriers (20%) younger than five were overweight or obese. Males exhibited more severe obesity than females. Thus, the obesity phenotype of 16p11.2 deletion carriers is of juvenile onset, exhibited an age- and gender-dependent penetrance. 16p11.2 deletion appears to predispose individuals to juvenile onset obesity and in this case are similar to the well-described Prader-Willi syndrome (PWS). Early detection of this deletion will provide opportunity to prevent obesity.
Collapse
Affiliation(s)
- Yongguo Yu
- Department of Laboratory Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | | | | | | |
Collapse
|
330
|
Lionel AC, Crosbie J, Barbosa N, Goodale T, Thiruvahindrapuram B, Rickaby J, Gazzellone M, Carson AR, Howe JL, Wang Z, Wei J, Stewart AFR, Roberts R, McPherson R, Fiebig A, Franke A, Schreiber S, Zwaigenbaum L, Fernandez BA, Roberts W, Arnold PD, Szatmari P, Marshall CR, Schachar R, Scherer SW. Rare Copy Number Variation Discovery and Cross-Disorder Comparisons Identify Risk Genes for ADHD. Sci Transl Med 2011; 3:95ra75. [DOI: 10.1126/scitranslmed.3002464] [Citation(s) in RCA: 264] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
331
|
Abstract
Autism is an etiologically and clinically heterogeneous group of disorders, diagnosed solely by the complex behavioral phenotype. On the basis of the high-heritability index, geneticists are confident that autism will be the first behavioral disorder for which the genetic basis can be well established. Although it was initially assumed that major genome-wide and candidate gene association studies would lead most directly to common autism genes, progress has been slow. Rather, most discoveries have come from studies of known genetic disorders associated with the behavioral phenotype. New technology, especially array chromosomal genomic hybridization, has both increased the identification of putative autism genes and raised to approximately 25%, the percentage of children for whom an autism-related genetic change can be identified. Incorporating clinical geneticists into the diagnostic and autism research arenas is vital to the field. Interpreting this new technology and deciphering autism's genetic montage require the skill set of the clinical geneticist including knowing how to acquire and interpret family pedigrees, how to analyze complex morphologic, neurologic, and medical phenotypes, sorting out heterogeneity, developing rational genetic models, and designing studies. The current emphasis on deciphering autism spectrum disorders has accelerated the field of neuroscience and demonstrated the necessity of multidisciplinary research that must include clinical geneticists both in the clinics and in the design and implementation of basic, clinical, and translational research.
Collapse
|
332
|
Carmona-Mora P, Walz K. Retinoic Acid Induced 1, RAI1: A Dosage Sensitive Gene Related to Neurobehavioral Alterations Including Autistic Behavior. Curr Genomics 2011; 11:607-17. [PMID: 21629438 PMCID: PMC3078685 DOI: 10.2174/138920210793360952] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Revised: 10/08/2010] [Accepted: 10/21/2010] [Indexed: 12/15/2022] Open
Abstract
Genomic structural changes, such as gene Copy Number Variations (CNVs) are extremely abundant in the human genome. An enormous effort is currently ongoing to recognize and catalogue human CNVs and their associations with abnormal phenotypic outcomes. Recently, several reports related neuropsychiatric diseases (i.e. autism spectrum disorders, schizophrenia, mental retardation, behavioral problems, epilepsy) with specific CNV. Moreover, for some conditions, both the deletion and duplication of the same genomic segment are related to the phenotype. Syndromes associated with CNVs (microdeletion and microduplication) have long been known to display specific neurobehavioral traits. It is important to note that not every gene is susceptible to gene dosage changes and there are only a few dosage sensitive genes. Smith-Magenis (SMS) and Potocki-Lupski (PTLS) syndromes are associated with a reciprocal microdeletion and microduplication within chromosome 17p11.2. in humans. The dosage sensitive gene responsible for most phenotypes in SMS has been identified: the Retinoic Acid Induced 1 (RAI1). Studies on mouse models and humans suggest that RAI1 is likely the dosage sensitive gene responsible for clinical features in PTLS. In addition, the human RAI1 gene has been implicated in several neurobehavioral traits as spinocerebellar ataxia (SCA2), schizophrenia and non syndromic autism. In this review we discuss the evidence of RAI1 as a dosage sensitive gene, its relationship with different neurobehavioral traits, gene structure and mutations, and what is known about its molecular and cellular function, as a first step in the elucidation of the mechanisms that relate dosage sensitive genes with abnormal neurobehavioral outcomes.
Collapse
Affiliation(s)
- Paulina Carmona-Mora
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | | |
Collapse
|
333
|
Pang ZP, Bacaj T, Yang X, Zhou P, Xu W, Südhof TC. Doc2 supports spontaneous synaptic transmission by a Ca(2+)-independent mechanism. Neuron 2011; 70:244-51. [PMID: 21521611 PMCID: PMC3102832 DOI: 10.1016/j.neuron.2011.03.011] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2011] [Indexed: 11/24/2022]
Abstract
Two families of Ca(2+)-binding proteins have been proposed as Ca(2+) sensors for spontaneous release: synaptotagmins and Doc2s, with the intriguing possibility that Doc2s may represent high-affinity Ca(2+) sensors that are activated by deletion of synaptotagmins, thereby accounting for the increased spontaneous release in synaptotagmin-deficient synapses. Here, we use an shRNA-dependent quadruple knockdown of all four Ca(2+)-binding proteins of the Doc2 family to confirm that Doc2-deficient synapses exhibit a marked decrease in the frequency of spontaneous release events. Knockdown of Doc2s in synaptotagmin-1-deficient synapses, however, failed to reduce either the increased spontaneous release or the decreased evoked release of these synapses, suggesting that Doc2s do not constitute Ca(2+) sensors for asynchronous release. Moreover, rescue experiments revealed that the decrease in spontaneous release induced by the Doc2 knockdown in wild-type synapses is fully reversed by mutant Doc2B lacking Ca(2+)-binding sites. Thus, our data suggest that Doc2s are modulators of spontaneous synaptic transmission that act by a Ca(2+)-independent mechanism.
Collapse
Affiliation(s)
- Zhiping P Pang
- Department of Molecular and Cellular Physiology, Stanford University, 265 Campus Drive, Stanford, CA 94305-5453, USA
| | | | | | | | | | | |
Collapse
|
334
|
Scherer SW, Dawson G. Risk factors for autism: translating genomic discoveries into diagnostics. Hum Genet 2011; 130:123-48. [PMID: 21701786 DOI: 10.1007/s00439-011-1037-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2011] [Accepted: 06/06/2011] [Indexed: 01/06/2023]
Abstract
Autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in communication and reciprocal social interaction, and the presence of restricted and repetitive behaviors. The spectrum of autistic features is variable, with severity of symptoms ranging from mild to severe, sometimes with poor clinical outcomes. Twin and family studies indicate a strong genetic basis for ASD susceptibility. Recent progress in defining rare highly penetrant mutations and copy number variations as ASD risk factors has prompted early uptake of these research findings into clinical diagnostics, with microarrays becoming a 'standard of care' test for any ASD diagnostic work-up. The ever-changing landscape of the generation of genomic data coupled with the vast heterogeneity in cause and expression of ASDs (further influenced by issues of penetrance, variable expressivity, multigenic inheritance and ascertainment) creates complexity that demands careful consideration of how to apply this knowledge. Here, we discuss the scientific, ethical, policy and communication aspects of translating the new discoveries into clinical and diagnostic tools for promoting the well-being of individuals and families with ASDs.
Collapse
Affiliation(s)
- Stephen W Scherer
- McLaughlin Centre and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada.
| | | |
Collapse
|
335
|
Swaminathan S, Kim S, Shen L, Risacher SL, Foroud T, Pankratz N, Potkin SG, Huentelman MJ, Craig DW, Weiner MW, Saykin AJ, The Alzheimer's Disease Neuroimaging Initiative Adni. Genomic Copy Number Analysis in Alzheimer's Disease and Mild Cognitive Impairment: An ADNI Study. Int J Alzheimers Dis 2011; 2011:729478. [PMID: 21660214 PMCID: PMC3109875 DOI: 10.4061/2011/729478] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 12/22/2010] [Accepted: 01/27/2011] [Indexed: 12/17/2022] Open
Abstract
Copy number variants (CNVs) are DNA sequence alterations, resulting in gains (duplications) and losses (deletions) of genomic segments. They often overlap genes and may play important roles in disease. Only one published study has examined CNVs in late-onset Alzheimer's disease (AD), and none have examined mild cognitive impairment (MCI). CNV calls were generated in 288 AD, 183 MCI, and 184 healthy control (HC) non-Hispanic Caucasian Alzheimer's Disease Neuroimaging Initiative participants. After quality control, 222 AD, 136 MCI, and 143 HC participants were entered into case/control association analyses, including candidate gene and whole genome approaches. Although no excess CNV burden was observed in cases (AD and/or MCI) relative to controls (HC), gene-based analyses revealed CNVs overlapping the candidate gene CHRFAM7A, as well as CSMD1, SLC35F2, HNRNPCL1, NRXN1, and ERBB4 regions, only in cases. Replication in larger samples is important, after which regions detected here may be promising targets for resequencing.
Collapse
Affiliation(s)
- Shanker Swaminathan
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
336
|
Zahir FR, Brown CJ. Epigenetic impacts on neurodevelopment: pathophysiological mechanisms and genetic modes of action. Pediatr Res 2011; 69:92R-100R. [PMID: 21293311 DOI: 10.1203/pdr.0b013e318213565e] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Disruptions of genes that are involved in epigenetic functions are known to be causative for several mental retardation/intellectual disability (MR/ID) syndromes. Recent work has highlighted genes with epigenetic functions as being implicated in autism spectrum disorders (ASDs) and schizophrenia (SCZ). The gene-environment interaction is an important factor of pathogenicity for these complex disorders. Epigenetic modifications offer a mechanism by which we can explain how the environment interacts with, and is able to dynamically regulate, the genome. This review aims to provide an overview of the role of epigenetic deregulation in the etiopathology for neurodevelopment disease.
Collapse
Affiliation(s)
- Farah R Zahir
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.
| | | |
Collapse
|
337
|
Barge-Schaapveld DQ, Maas SM, Polstra A, Knegt LC, Hennekam RC. The atypical 16p11.2 deletion: A not so atypical microdeletion syndrome? Am J Med Genet A 2011; 155A:1066-72. [DOI: 10.1002/ajmg.a.33991] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 02/15/2011] [Indexed: 01/19/2023]
|
338
|
|
339
|
Current World Literature. Curr Opin Neurol 2011; 24:183-90. [DOI: 10.1097/wco.0b013e32834585ec] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
340
|
Abstract
Molecular genetic research, building on genetic epidemiology, has provided the field of psychiatry with a host of exciting advances. It is now clear beyond any reasonable doubt that genetic inheritance influences liability to develop almost every major psychiatric disorder. Rapid progress in identifying genes contributing to psychiatric liability, recently accelerated by the advent of approaches such as genome-wide association studies and chromosomal microarray analysis, raises a critical question for psychiatric practice and training: how will molecular genetics alter the practice of psychiatry for front-line clinicians? The premise of the present review is that our growing knowledge regarding the roles of copy number variants in behavioral disorders will soon require revision of standards of evaluation and care for psychiatric patients.
Collapse
Affiliation(s)
- Daniel Moreno-De-Luca
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta, GA 30322, USA
| | - Joseph F. Cubells
- Departments of Human Genetics and Psychiatry and Behavioral Sciences, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta, GA 30322, USA,
| |
Collapse
|
341
|
Konialis C, Hagnefelt B, Sevastidou S, Karapanou S, Pispili K, Markaki A, Pangalos C. Uncovering recurrent microdeletion syndromes and subtelomeric deletions/duplications through non-selective application of a MLPA-based extended prenatal panel in routine prenatal diagnosis. Prenat Diagn 2011; 31:571-7. [DOI: 10.1002/pd.2750] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2010] [Revised: 12/27/2010] [Accepted: 12/30/2010] [Indexed: 11/09/2022]
|
342
|
Levinson DF, Duan J, Oh S, Wang K, Sanders AR, Shi J, Zhang N, Mowry BJ, Olincy A, Amin F, Cloninger CR, Silverman JM, Buccola NG, Byerley WF, Black DW, Kendler KS, Freedman R, Dudbridge F, Pe’er I, Hakonarson H, Bergen SE, Fanous AH, Holmans PA, Gejman PV. Copy number variants in schizophrenia: confirmation of five previous findings and new evidence for 3q29 microdeletions and VIPR2 duplications. Am J Psychiatry 2011; 168:302-16. [PMID: 21285140 PMCID: PMC4441324 DOI: 10.1176/appi.ajp.2010.10060876] [Citation(s) in RCA: 332] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To evaluate previously reported associations of copy number variants (CNVs) with schizophrenia and to identify additional associations, the authors analyzed CNVs in the Molecular Genetics of Schizophrenia study (MGS) and additional available data. METHOD After quality control, MGS data for 3,945 subjects with schizophrenia or schizoaffective disorder and 3,611 screened comparison subjects were available for analysis of rare CNVs (<1% frequency). CNV detection thresholds were chosen that maximized concordance in 151 duplicate assays. Pointwise and genewise analyses were carried out, as well as analyses of previously reported regions. Selected regions were visually inspected and confirmed with quantitative polymerase chain reaction. RESULTS In analyses of MGS data combined with other available data sets, odds ratios of 7.5 or greater were observed for previously reported deletions in chromosomes 1q21.1, 15q13.3, and 22q11.21, duplications in 16p11.2, and exon-disrupting deletions in NRXN1. The most consistently supported candidate associations across data sets included a 1.6-Mb deletion in chromosome 3q29 (21 genes, TFRC to BDH1) that was previously described in a mild-moderate mental retardation syndrome, exonic duplications in the gene for vasoactive intestinal peptide receptor 2 (VIPR2), and exonic duplications in C16orf72. The case subjects had a modestly higher genome-wide number of gene-containing deletions (>100 kb and >1 Mb) but not duplications. CONCLUSIONS The data strongly confirm the association of schizophrenia with 1q21.1, 15q13.3, and 22q11.21 deletions, 16p11.2 duplications, and exonic NRXN1 deletions. These CNVs, as well as 3q29 deletions, are also associated with mental retardation, autism spectrum disorders, and epilepsy. Additional candidate genes and regions, including VIPR2, were identified. Study of the mechanisms underlying these associations should shed light on the pathophysiology of schizophrenia.
Collapse
|
343
|
Shen Y, Chen X, Wang L, Guo J, Shen J, An Y, Zhu H, Zhu Y, Xin R, Bao Y, Gusella JF, Zhang T, Wu BL. Intra-family phenotypic heterogeneity of 16p11.2 deletion carriers in a three-generation Chinese family. Am J Med Genet B Neuropsychiatr Genet 2011; 156:225-32. [PMID: 21302351 DOI: 10.1002/ajmg.b.31147] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 10/26/2010] [Indexed: 11/10/2022]
Abstract
The 16p11.2 deletion is a recurrent genomic event and a significant risk factor for autism spectrum disorders (ASD). This genomic disorder also exhibits extensive phenotypic variability and diverse clinical phenotypes. The full extent of phenotypic heterogeneity associated with the 16p11.2 deletion disorder and the factors that modify the clinical phenotypes are currently unknown. Multiplex families with deletion offer unique opportunities for exploring the degree of heterogeneity and implicating modifiers. Here we reported the clinical and genomic characteristics of three 16p11.2 deletion carriers in a Chinese family. The father carries a de novo 16p11.2 deletion, and it was transmitted to the proband and sib. The proband presented with ASD, intellectual disability, learning difficulty, congenital malformations such as atrial septal defect, scoliosis. His dysmorphic features included myopia and strabismus, flat and broad nasal bridge, etc. While the father shared same neurodevelopmental problems as the proband, the younger brother did not show many of the proband's phenotypes. The possible unmasked mutation of TBX6 and MVP gene in this deleted region and the differential distribution of other genomic CNVs were explored to explain the phenotypic heterogeneity in these carriers. This report demonstrated the different developmental trajectory and discordant phenotypes among family members with the same 16p11.2 deletion, thus further illustrated the phenotypic complexity and heterogeneity of the 16p11.2 deletion.
Collapse
Affiliation(s)
- Yiping Shen
- Department of Laboratory Medicine, Children's Hospital Boston, Boston, Massachusetts, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
344
|
Nik-Zainal S, Strick R, Storer M, Huang N, Rad R, Willatt L, Fitzgerald T, Martin V, Sandford R, Carter NP, Janecke AR, Renner SP, Oppelt PG, Oppelt P, Schulze C, Brucker S, Hurles M, Beckmann MW, Strissel PL, Shaw-Smith C. High incidence of recurrent copy number variants in patients with isolated and syndromic Müllerian aplasia. J Med Genet 2011; 48:197-204. [PMID: 21278390 PMCID: PMC3322361 DOI: 10.1136/jmg.2010.082412] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Congenital malformations involving the Müllerian ducts are observed in around 5% of infertile women. Complete aplasia of the uterus, cervix, and upper vagina, also termed Müllerian aplasia or Mayer-Rokitansky-Kuster-Hauser (MRKH) syndrome, occurs with an incidence of around 1 in 4500 female births, and occurs in both isolated and syndromic forms. Previous reports have suggested that a proportion of cases, especially syndromic cases, are caused by variation in copy number at different genomic loci. METHODS In order to obtain an overview of the contribution of copy number variation to both isolated and syndromic forms of Müllerian aplasia, copy number assays were performed in a series of 63 cases, of which 25 were syndromic and 38 isolated. RESULTS A high incidence (9/63, 14%) of recurrent copy number variants in this cohort is reported here. These comprised four cases of microdeletion at 16p11.2, an autism susceptibility locus not previously associated with Müllerian aplasia, four cases of microdeletion at 17q12, and one case of a distal 22q11.2 microdeletion. Microdeletions at 16p11.2 and 17q12 were found in 4/38 (10.5%) cases with isolated Müllerian aplasia, and at 16p11.2, 17q12 and 22q11.2 (distal) in 5/25 cases (20%) with syndromic Müllerian aplasia. CONCLUSION The finding of microdeletion at 16p11.2 in 2/38 (5%) of isolated and 2/25 (8%) of syndromic cases suggests a significant contribution of this copy number variant alone to the pathogenesis of Müllerian aplasia. Overall, the high incidence of recurrent copy number variants in all forms of Müllerian aplasia has implications for the understanding of the aetiopathogenesis of the condition, and for genetic counselling in families affected by it.
Collapse
Affiliation(s)
| | - Reiner Strick
- University-Clinic Erlangen, Department of Obstetrics and Gynecology, Erlangen, Germany
| | - Mekayla Storer
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Institute of Child Health, London, UK
| | - Ni Huang
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Roland Rad
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Lionel Willatt
- Regional Cytogenetics Laboratory, Addenbrooke’s Hospital, Cambridge, UK
| | | | - Vicki Martin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Institute of Child Health, London, UK
| | - Richard Sandford
- Department of Clinical Genetics, Addenbrooke’s Hospital, Cambridge, UK
| | | | - Andreas R Janecke
- Department of Pediatrics II, Innsbruck Medical University, Innsbruck, Austria
- Division of Human Genetics, Innsbruck Medical University, Innsbruck, Austria
| | - Stefan P Renner
- University-Clinic Erlangen, Department of Obstetrics and Gynecology, Erlangen, Germany
| | - Patricia G Oppelt
- University-Clinic Erlangen, Department of Obstetrics and Gynecology, Erlangen, Germany
| | - Peter Oppelt
- University-Clinic Erlangen, Department of Obstetrics and Gynecology, Erlangen, Germany
| | - Christine Schulze
- University-Clinic Erlangen, Department of Obstetrics and Gynecology, Erlangen, Germany
| | - Sara Brucker
- University-Clinic, Department of Obstetrics and Gynecology, Tübingen, Germany
| | | | - Matthias W Beckmann
- University-Clinic Erlangen, Department of Obstetrics and Gynecology, Erlangen, Germany
| | - Pamela L Strissel
- University-Clinic Erlangen, Department of Obstetrics and Gynecology, Erlangen, Germany
| | - Charles Shaw-Smith
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Institute of Child Health, London, UK
- Institute of Biomedical and Clinical Science, Peninsula College of Medicine and Dentistry, University of Exeter, Barrack Road, Exeter EX2 5DW, UK
| |
Collapse
|
345
|
Liu P, Erez A, Nagamani SCS, Bi W, Carvalho CMB, Simmons AD, Wiszniewska J, Fang P, Eng PA, Cooper ML, Sutton VR, Roeder ER, Bodensteiner JB, Delgado MR, Prakash SK, Belmont JW, Stankiewicz P, Berg JS, Shinawi M, Patel A, Cheung SW, Lupski JR. Copy number gain at Xp22.31 includes complex duplication rearrangements and recurrent triplications. Hum Mol Genet 2011; 20:1975-88. [PMID: 21355048 DOI: 10.1093/hmg/ddr078] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Genomic instability is a feature of the human Xp22.31 region wherein deletions are associated with X-linked ichthyosis, mental retardation and attention deficit hyperactivity disorder. A putative homologous recombination hotspot motif is enriched in low copy repeats that mediate recurrent deletion at this locus. To date, few efforts have focused on copy number gain at Xp22.31. However, clinical testing revealed a high incidence of duplication of Xp22.31 in subjects ascertained and referred with neurobehavioral phenotypes. We systematically studied 61 unrelated subjects with rearrangements revealing gain in copy number, using multiple molecular assays. We detected not only the anticipated recurrent and simple nonrecurrent duplications, but also unexpectedly identified recurrent triplications and other complex rearrangements. Breakpoint analyses enabled us to surmise the mechanisms for many of these rearrangements. The clinical significance of the recurrent duplications and triplications were assessed using different approaches. We cannot find any evidence to support pathogenicity of the Xp22.31 duplication. However, our data suggest that the Xp22.31 duplication may serve as a risk factor for abnormal phenotypes. Our findings highlight the need for more robust Xp22.31 triplication detection in that such further gain may be more penetrant than the duplications. Our findings reveal the distribution of different mechanisms for genomic duplication rearrangements at a given locus, and provide insights into aspects of strand exchange events between paralogous sequences in the human genome.
Collapse
Affiliation(s)
- Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX 77030, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
346
|
Miller DT. Genetic testing for autism: recent advances and clinical implications. Expert Rev Mol Diagn 2011; 10:837-40. [PMID: 20964600 DOI: 10.1586/erm.10.82] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
347
|
Copy number variation in the dosage-sensitive 16p11.2 interval accounts for only a small proportion of autism incidence: A systematic review and meta-analysis. Genet Med 2011; 13:377-84. [DOI: 10.1097/gim.0b013e3182076c0c] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
|
348
|
van Bon BWM, Balciuniene J, Fruhman G, Nagamani SCS, Broome DL, Cameron E, Martinet D, Roulet E, Jacquemont S, Beckmann JS, Irons M, Potocki L, Lee B, Cheung SW, Patel A, Bellini M, Selicorni A, Ciccone R, Silengo M, Vetro A, Knoers NV, de Leeuw N, Pfundt R, Wolf B, Jira P, Aradhya S, Stankiewicz P, Brunner HG, Zuffardi O, Selleck SB, Lupski JR, de Vries BBA. The phenotype of recurrent 10q22q23 deletions and duplications. Eur J Hum Genet 2011; 19:400-8. [PMID: 21248748 DOI: 10.1038/ejhg.2010.211] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The genomic architecture of the 10q22q23 region is characterised by two low-copy repeats (LCRs3 and 4), and deletions in this region appear to be rare. We report the clinical and molecular characterisation of eight novel deletions and six duplications within the 10q22.3q23.3 region. Five deletions and three duplications occur between LCRs3 and 4, whereas three deletions and three duplications have unique breakpoints. Most of the individuals with the LCR3-4 deletion had developmental delay, mainly affecting speech. In addition, macrocephaly, mild facial dysmorphisms, cerebellar anomalies, cardiac defects and congenital breast aplasia were observed. For congenital breast aplasia, the NRG3 gene, known to be involved in early mammary gland development in mice, is a putative candidate gene. For cardiac defects, BMPR1A and GRID1 are putative candidate genes because of their association with cardiac structure and function. Duplications between LCRs3 and 4 are associated with variable phenotypic penetrance. Probands had speech and/or motor delays and dysmorphisms including a broad forehead, deep-set eyes, upslanting palpebral fissures, a smooth philtrum and a thin upper lip. In conclusion, duplications between LCRs3 and 4 on 10q22.3q23.2 may lead to a distinct facial appearance and delays in speech and motor development. However, the phenotypic spectrum is broad, and duplications have also been found in healthy family members of a proband. Reciprocal deletions lead to speech and language delay, mild facial dysmorphisms and, in some individuals, to cerebellar, breast developmental and cardiac defects.
Collapse
Affiliation(s)
- Bregje W M van Bon
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
349
|
de Leeuw N, Hehir-Kwa JY, Simons A, Geurts van Kessel A, Smeets DF, Faas BHW, Pfundt R. SNP Array Analysis in Constitutional and Cancer Genome Diagnostics – Copy Number Variants, Genotyping and Quality Control. Cytogenet Genome Res 2011; 135:212-21. [PMID: 21934286 DOI: 10.1159/000331273] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- N de Leeuw
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|
350
|
Lichtenbelt K, Knoers N, Schuring-Blom G. From Karyotyping to Array-CGH in Prenatal Diagnosis. Cytogenet Genome Res 2011; 135:241-50. [DOI: 10.1159/000334065] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
|